add sensitivity analysis to IBD example

R/sensitivity.R

@@ -393,6 +393,26 @@ covariance_matrix <- function(model, confound_ix = NULL, rho = 0.0) {
 #' @param progress A logical indicating whether to show a progress bar.
 #' @return A `date.frame` giving the outputs of `indirect_overall` across many
 #'   values of the correlation rho.
+#' @examples
+#' xy_data <- demo_spline()
+#' exper <- mediation_data(
+#'     xy_data, starts_with("outcome"), "treatment", "mediator"
+#' )
+#' model <- multimedia(
+#'     exper,
+#'     outcome_estimator = glmnet_model(lambda = 1e-2)
+#' ) |>
+#'     estimate(exper)
+#' rho_seq <- c(-0.2, 0.2)
+#' perturb <- matrix(
+#'     c(
+#'         0, 3, 0,
+#'         3, 0, 0,
+#'         0, 0, 0
+#'     ),
+#'     nrow = 3, byrow = TRUE
+#' )
+#' sensitivity_perturb(model, exper, perturb, n_bootstrap = 2)
 #' @export
 sensitivity_perturb <- function(
     model, exper, perturb, nu_seq = NULL, n_bootstrap = 100, progress = TRUE) {

vignettes/IBD.Rmd

@@ -276,6 +276,15 @@ ggplot(coords) +
     facet_wrap(~ type + reorder(outcome, -abundance))
 ```
 
+```{r}
+confound_ix <- data.frame(
+    outcome = vis_outcomes,
+    mediator = "gEnterocloster"
+)
+sensitivity_overall <- sensitivity(model, exper, confound_ix)
+saveRDS(sensitivity_overall, "~/Downloads/sensitivity_overall-IBD.rds")
+```
+
 Pathwise indirect effects are those that appear when modifying the treatment
 status for a single mediator. Unlike overall indirect effects, they give us
 effects for individual mediator-outcome pairs. Now, instead of averaging over
@@ -387,11 +396,13 @@ p1 | p2
 ```{r}
 confound_ix <- data.frame(
     mediator = c("gEnterocloster", "gEnterocloster", "gCAG103"),
-    outcome = c("m1129_chenodeoxycholate", "m1403_cholate", "m0900_ketodeoxycholate")
+    outcome = c(
+        "m1129_chenodeoxycholate", "m1403_cholate", "m0900_ketodeoxycholate"
+    )
 )
 
-rho_seq <- seq(-0.7, 0.7, length.out = 2)
-sensitivity_analysis <- sensitivity_pathwise(model, exper, confound_ix)#, rho_seq = rho_seq)
+sensitivity_pathwise <- sensitivity_pathwise(model, exper, confound_ix)
+saveRDS(sensitivity_pathwise, "~/Downloads/sensitivity_pathwise-IBD.rds")
 ```
 
 # Hurdle-Lognormal Approach